December 2005 - modeller_usage

Re: To Model missing domains in the content of the rest
by Shirley Li 08 Dec '05

08 Dec '05

Dear MODELLER experts, I have a target protein, whose X-ray structure is PARTIALLY available (the middle part, named domain B). There are two big regions missing (domain A & C) in the crystal structure, with more than 50 residues in each I would like to use MODELLER to model domain A & C, and there are templates available. I wonder if it is possible to include THE CONTENT OF domain B. in another word, to create a complete model of A-B-C while keep the coordinates of B domain fixed. Any help/information will be greatly appreciated. Shirley --------------------------------- __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com

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To use separate templates for different region of a protein
by Shirley Li 08 Dec '05

08 Dec '05

Dear All, With MODELLER, I wonder if it is possible to use different template(s) for different region of one target protein. For example, One protein has domain 1, 2 and 3. I would like to construct a complete model of this protein, with templates A and B for domain 1, templates C,D,and E for domain 3, and domain 2 already has coordinates/structure, which need to be preserved in the complete model. Is there any way to do the above? If so, how? I tried to use the "inifile" feature and use the existing coordinate file of domain 2 as "inifile". while I got error message of " Atom index is out of range (iatm,natm)". Any help/information will be very much appreciated. Shirley --------------------------------- Yahoo! Shopping Find Great Deals on Holiday Gifts at Yahoo! Shopping

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file name problem
by Starr Hazard 08 Dec '05

08 Dec '05

Folks, The following lines: mdl.assess_dope(output='ENERGY_PROFILE NO_REPORT', file=code+'.profile', normalize_profile=True, smoothing_window=15) are producing output files with a question mark in the name string. ABC31_HUMAN.BL09950001.pdb?.profile The question mark renders cp, mv and rename incapable of doing anything with the file. Is there a way to prevent modeller from appending the question mark to the created files? Thanks, Starr

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Re: [modeller_usage] How to choose the best model?
by ��¨Ե��ط�� Ե��͹�� 07 Dec '05

07 Dec '05

Dear Modeller users For my research the parameter which i should consider for the best model is from the evaluated program such as PROSA PROCHECK or Verify3D. For Procheck , i use the model which give a quaility of model within >80% core regions. That i used in my project so if any recomments for my research please contact me. Thank Mr. JItrayut Jitonnom CSML Chiang Mai University Thailand -----Original Message----- From: carromeu(a)usp.br Sent: Fri, 02 Dec 2005 21:41:42 -0200 To: modeller_usage(a)salilab.org Subject: [modeller_usage] How to choose the best model? > Dear Modeller users, > > I'm generating diverses models to my protein (400 - is this to great?). >However I don't know how is the best parameter to look when choosing the best >model. Objective function from Modeller, ProCheck parameters, Energy >parameters... What parameters you use and why? If using Ramachandran plot as a >discriminative parameter, how great must be the parameters calculated (for >example: >90% in favored regions, ---------------------------------------------------------------------------------- http://www.chaiyo.com ไชโยเมล์ - ฟรีอีเมล์รูปแบบใหม่ สดใสกว่าเดิม...

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How to include alignment to model_symmetry_define()
by bmbbl＠leeds.ac.uk 07 Dec '05

07 Dec '05

Hi Modellers, I need to obtain loop conformation distributions in a tetramer structure. So I used loopmodel() to redefine the 4 loops in each subunit. I found that the 4 loops in each tetramer is not symmetrical. I therefore applied model_symmetry_define() in order to fix them the same during the optimisation. Here I have a question. The code I have used is at http://salilab.org/modeller/manual/node160.html However, in define_symmetry-3.atm file, the structure looks very bizarre. It has lost its secondary structure elements and 4 loops are not symmetrical at all. So I tried to add the sequence alignment between the loop model and the template. I cannot work out the python code. Could some one kindly have a look what I have done wrongly please. Here is the code: # Example for: model.symmetry.define() # This will force two copies of RCK4 to have similar mainchain # conformation. log.level(1, 1, 1, 1, 0) env = environ() env.libs.topology.read(file='$(LIB)/top_heav.lib') env.libs.parameters.read(file='$(LIB)/par.lib') #env.io.atom_files_directory = 'xxx' env.io.atom_files_directory = '.' def defsym(lop, aln, seg1, seg2): for (set, seg) in [(2, seg1), (3, seg2)]: lop.pick_atoms(aln, pick_atoms_set=set, selection_segment=seg, atom_types='All', selection_status='INITIALIZE', selection_search='SEGMENT') lop.symmetry.define(symmetry_weight=1.0, add_symmetry=(True, False)) # Generate two copies of a segment: lop = model(env, file='model-nam', model_segment=('1:A', '110:D')) aln = alignment(env) aln.append_model(lop, align_codes='model-nam', atom_files='tmp-nam') aln.append_model(lop, align_codes='model-nam'+'_ini', atom_files='tmp-nam'+'_ini') lop.generate_topology(aln, sequence='model-nam'+'_ini') lop.transfer_xyz(aln) lop.build(initialize_xyz=False, build_method='INTERNAL_COORDINATES') #lop.rename_segments(segment_ids=('A', 'B')) #, renumber_residues=(1, 1)) myedat = energy_data(dynamic_sphere = False) lop.energy(edat=myedat) lop.randomize_xyz(deviation=6.0) # Define the two segments (chains in this case) to be identical: defsym(lop, aln, seg1=('39:A', '49:A'), seg2=('39:B', '49:B')) # Make them identical by optimizing the initial randomized structure # without any other restraints: lop.energy(edat=myedat) lop.write(file='define_symmetry-1.atm') lop.optimize(max_iterations=300, edat=myedat) lop.write(file='define_symmetry-2.atm') lop.energy(edat=myedat) # Now optimize with stereochemical restraints so that the # result is not so distorted a structure (still distorted # because optimization is not thorough): myedat.dynamic_sphere = True lop.restraints.make(aln, restraint_type='stereo', spline_on_site=False, edat=myedat) lop.randomize_xyz(deviation=3.0) for method in (1, 3, 1): # 1 = conjugate gradients, 3 = molecular dynamics lop.optimize(max_iterations=300, md_return='FINAL', edat=myedat, optimization_method=method, output='REPORT') lop.write(file='define_symmetry-3.atm') lop.energy(edat=myedat) # Create a blank alignment so that superpose uses its 1:1 default aln = alignment(env) lop = model(env, file='define_symmetry-3.atm', model_segment=('39:A', '49:A')) lop2 = model(env, file='define_symmetry-3.atm', model_segment=('39:B', '49:B')) lop.pick_atoms(aln, atom_types='All') lop.superpose(lop2, aln) Also, what does aln.append_model(lop, align_codes='model-nam'+'_ini', atom_files='tmp-nam'+'_ini') mean? The erro message by executing the above .py file is: "_modeller.error: transfe_682E> Structural information is not available for all sequences in the alignment. Aborting." Thank you very much. Binbin

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The large gap on sequence is a big problem
by ��¨Ե��ط�� Ե��͹�� 07 Dec '05

07 Dec '05

Dear Modeller users I have a big problem in my sequence which has a long gap when i make a multiple alignment so how modeller solve this problem. Is it built this model from this gap? or we should cut this gap(but i don't want to cut this sequence because this sequence is important for looking the catalytic mechanism. Can any one help me please contact me?. Thank you Mr. Jitrayut Jitonnom CSML (Computer Simulation and Modeling Laboratory) Chiang Mai University Thailand. ---------------------------------------------------------------------------------- http://www.chaiyo.com ไชโยเมล์ - ฟรีอีเมล์รูปแบบใหม่ สดใสกว่าเดิม...

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General Homolgy question
by Yogesh Sabnis 07 Dec '05

07 Dec '05

Hello, I have a general question on Comparative Protein Modeling. Is the modeling of only the active site residues, having a seq. identity of 80% with another sequence of a 3D structure, better than modeling the entire protein (seq. identity ~ 50%)? What are the disadvantages of modeling only certain seqments of a protein, active site mainly? When is this desirable rather than modeling the entire protein? Thank you. Kind regards, Yogesh Yogesh Sabnis Ph.D Dept. Medicinal Chemistry Uppsala University BMC, Box 574 Uppsala, SE-753 31 Sweden Phone: 0046 (0)18 4715012 Fax: 0046 (0)18 4714474

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dynamic memory allocation failed
by Ilya Shlyakhter 05 Dec '05

05 Dec '05

Dear Modeller users, I'm getting a "dynamic memory allocation failed" message on a very small model. The test examples work fine, but when I modify model-full.py for my own use it gives a problem. Below I give the files I used, and the error message. I would appreciate any suggestions. Ilya model-full-test.py: ------------------------------------------------------------ # A sample script for fully automated comparative modeling from modeller.automodel import * # Load the automodel class log.verbose() env = environ() # directories for input atom files env.io.atom_files_directory = './' a = automodel(env, # file with template codes and target sequence alnfile = 'myalign.seg', # PDB codes of the templates knowns = ('1fjk', '1yod'), # code of the target sequence = '1qqq') a.auto_align() # get an automatic alignment a.make() # do homology modelling ------------------------------------------------------------ myalign.seg: >P1;1qqq sequence:1qqq:FIRST:@:52:@:phospholamban:Homo sapiens: 0:0 MDKVQYLTRSAIRRASTIEMPQQARQKLQNLYINRCLREICQELKEIRAMLK* >P1;1fjk structureN:1fjk:1:A:52:A:phospholamban:Homo sapiens:0:0 * >P1;1yod structureX:1yod:1:B:51:B:phospholamban:Homo sapiens: 1.80:0 ------------------------------------------------------------ 1fjk.pdb and 1yod.pdb files, downloaded from the PDB, are in the current dir. model-full-test.log: -------------------------------------- Kind, OS, HostName, Kernel, Processor: 4, Linux optima 2.4.22-1.2199.nptl i686 Date and time of compilation : 06/20/2005 12:04:54 MODELLER executable type : i386-intel8 Job starting time (YY/MM/DD HH:MM:SS): 2005/12/05 02:01:13.119 openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/restyp.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/resdih.lib rdrdih__263_> Number of dihedral angle types : 9 Maximal number of dihedral angle optima: 3 Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/af_mnchdef.lib rdwilmo_274_> Mainchain residue conformation classes: APBLE openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch.lib rdclass_257_> Number of classes: 5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v1}/modlib/xs4.mat rdrrwgh_268_> Number of residue types: 21 runcmd______> alignment.append(align_codes=['1fjk', '1yod'], atom_files=[], file='myalign.seg', (def)remove_gaps=True, (def)alignme\ nt_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) openf___224_> Open myalign.seg openf5__224_> Open 13 OLD SEQUENTIAL ./1fjk.atm Dynamically allocated memory at amaxalignment [B,kB,MB]: 2124311 2074.522 2.026 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2125365 2075.552 2.027 Dynamically allocated memory at amaxalignment [B,kB,MB]: 2299585 2245.688 2.193 openf5__224_> Open 13 OLD SEQUENTIAL ./1yod.atm Read the alignment from file : myalign.seg Total number of alignment positions: 52 # Code #_Res #_Segm PDB_code Name ------------------------------------------------------------------------------- 1 1fjk 52 1 1fjk phospholamban 2 1yod 0 0 1yod phospholamban runcmd______> alignment.malign((def)rr_file='$(LIB)/as1.sim.mat', (def)off_diagonal=100, (def)local_alignment=False, (def)matrix_of\ fset=0.0, (def)overhang=0, (def)align_block=0, gap_penalties_1d=(-600, -400)) openf5__224_> Open 11 OLD SEQUENTIAL $(LIB)/as1.sim.mat rdrrwgh_268_> Number of residue types: 20 malign__215E> Dynamic memory allocation failed. Routine, variable, status: rrdst 3 --------------------------------------

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Re: modeller_usage Digest, Vol 4, Issue 107
by rathankar rao 02 Dec '05

02 Dec '05

helllo all i have a doubt in this context. while modelling the first model has a least energy what is the necessity for modelling 20 or 50 structures modeller_usage-request(a)salilab.org wrote: Send modeller_usage mailing list submissions to modeller_usage(a)salilab.org To subscribe or unsubscribe via the World Wide Web, visit http://salilab.org/mailman/listinfo/modeller_usage or, via email, send a message with subject or body 'help' to modeller_usage-request(a)salilab.org You can reach the person managing the list at modeller_usage-owner(a)salilab.org When replying, please edit your Subject line so it is more specific than "Re: Contents of modeller_usage digest..." Today's Topics: 1. restrain beta strands and plates (Arnout Voet) 2. RE: How many models to generate? (Frederico Arnoldi) 3. Re: RE: How many models to generate? (Charlotte Habegger-Polomat) 4. Re: max number of optima in resdih.lib (Modeller Caretaker) ---------------------------------------------------------------------- Message: 1 Date: Fri, 2 Dec 2005 13:53:24 +0100 From: Arnout Voet Subject: [modeller_usage] restrain beta strands and plates To: modeller_usage(a)salilab.org Message-ID: <1133528004.439043c4d754d(a)webmail1.kuleuven.be> Content-Type: text/plain; charset=ISO-8859-1 dear modellers i have met a problem in my scripting to restrain the secondary structure element beta sheet beta strand. For alpha helices it works and i see an influence on the modelled structure , however for sheets it does not work and i get the same model with or without the restraining in the script. Could somebody pleez help me with the exact restraining of it kind regards arnout voet phd student biochemistry kuleuven. Disclaimer: http://www.kuleuven.be/cwis/email_disclaimer.htm ------------------------------ Message: 2 Date: Fri, 02 Dec 2005 13:22:38 +0000 From: "Frederico Arnoldi" Subject: [modeller_usage] RE: How many models to generate? To: modeller_usage(a)salilab.org Message-ID: Content-Type: text/plain; charset=iso-8859-1; format=flowed Hello Charlotte Habegger-Polomat, I am not an expert modeller user, but what I can "share" about it? I think the number of models generated depends on available time and computational power you have to carry it. I usually generate between 100 and 200, and select that model with the lowest "current energy". Probably somebody could discuss it better, anyway, I tried ;) Frederico Arnoldi UNESP - Rio Claro - Brazil > >Dear Modeller users, > >I was wondering if others would share how many structures you usually >generate for a family of models. > >I am currently working on modelling my protein of interest with 3 known >template structures (>30% sequence similarity). When using Modeller, I >generate a family of 20 models and then evaluate the variability and >quality of models within the family. > >How many do other Modeller users generate? > >How do you decide on this number? > >I've read articles where 3 models, others where 30 models were generated >with Modeller... > >Thanks! > >-Charlotte Habegger-Polomat ------------------------------ Message: 3 Date: Fri, 02 Dec 2005 10:37:18 -0500 From: Charlotte Habegger-Polomat Subject: Re: [modeller_usage] RE: How many models to generate? To: modeller_usage(a)salilab.org Message-ID: <43906A2E.7090503(a)rsvs.ulaval.ca> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hello Frederico Arnoldi! Thanks for your answer...I have been generating 20 models for my protein of interest, and after evaluating the variability within the family of models, I select one or more models to work with. This reminds me that I have only an "approximation" of my structure, and also allows me to retain some variability. I then work with these models as one would work with a family of NMR structures. Does anyone else use more than one model to work with after generating a family with Modeller? Thank you! -Charlotte Habegger-Polomat Frederico Arnoldi wrote: > Hello Charlotte Habegger-Polomat, > > I am not an expert modeller user, but what I can "share" about it? > I think the number of models generated depends on available time and > computational power you have to carry it. I usually generate between > 100 and 200, and select that model with the lowest "current energy". > Probably somebody could discuss it better, anyway, I tried ;) > > Frederico Arnoldi > UNESP - Rio Claro - Brazil > > ------------------------------ Message: 4 Date: Fri, 02 Dec 2005 10:50:59 -0800 From: Modeller Caretaker Subject: Re: [modeller_usage] max number of optima in resdih.lib To: Luis Gracia Cc: modeller_usage(a)salilab.org Message-ID: <43909793.2030905(a)salilab.org> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Luis Gracia wrote: > Hi! I need to modify the rotamer definitions in resdih.lib, but I get > the following error when adding 4 entries to a residue. > > _modeller.error: rdrdih__223E> Internal error: array too small: MDIHOPT > current maximum, current need: 4 4 > > This is the line that creates the error: > > CA CB CG OD1 4 0.516 0.194 0.161 0.129 -11.9 69.4 > -67.6 154.8 12.5 11.1 23.3 25.7 -180 -90 -90 0 0 90 90 180 > > using only 3 optima values doesn't give any error. Is there a limit in > the maximum number of optima? This info is part of the output but I > don't know if its a limit or the number found: > Maximal number of dihedral angle optima: 3 Yes - unfortunately there is a hard-coded limit of 3 optima. This will be removed in the next release of Modeller, but for the time being, you are restricted to 3. Ben Webb, Modeller Caretaker -- modeller-care(a)salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage ------------------------------ _______________________________________________ modeller_usage mailing list modeller_usage(a)salilab.org http://salilab.org/mailman/listinfo/modeller_usage End of modeller_usage Digest, Vol 4, Issue 107 ********************************************** --------------------------------- Yahoo! Personals Single? There's someone we'd like you to meet. Lots of someones, actually. Yahoo! Personals

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How to choose the best model?
by carromeu＠usp.br 02 Dec '05

02 Dec '05

Dear Modeller users, I'm generating diverses models to my protein (400 - is this to great?). However I don't know how is the best parameter to look when choosing the best model. Objective function from Modeller, ProCheck parameters, Energy parameters... What parameters you use and why? If using Ramachandran plot as a discriminative parameter, how great must be the parameters calculated (for example: >90% in favored regions, <1% in disalowed regions)? Any help is welcome. Thanks for advice, Cassiano Carromeu.

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